| Class | Description |
|---|---|
| AtomActionTransformed |
Moves (translates) an atom by a specified vector amount.
|
| BetaPhaseLatticeParameter |
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
|
| BetaPhaseLatticeParameterLS |
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
for lattice sum, rC = 250 A
|
| BetaPhaseLatticeParameterNA |
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
|
| BoundaryDeformablePeriodicSwitch | |
| BoundaryRectangularPeriodicSwitch | |
| CalcAnalytical2ndDerivativeNitrogen |
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
|
| CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen |
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
|
| CalcNumerical2ndDerivative |
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
|
| CalcNumerical2ndDerivativeNitrogen |
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
|
| ConformationNitrogen |
Conformation for Nitrogen
Reference paper: Etters RD.
|
| ConformationNitrogenShellModel |
Conformation for Nitrogen (Shell Model)
Reference: Fabianski R.
|
| CoordinateDefinitionNitrogen |
CoordinateDefinition implementation for nitrogen molecule.
|
| CoordinateDefinitionNitrogen.OrientationAgentSource | |
| CoordinateDefinitionNitrogenSuperBox |
CoordinateDefinition implementation for nitrogen molecule.
|
| CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource | |
| FindBetaN2AngleFromParameter |
Class that creates:
1.
|
| FindPairMoleculeIndex |
Class to identify the pair of molecules that are the same in terms of displacement vector and orientation
This is done to speed up the construction of the Hessian Matrix such that we do not have to recalculate
the block matrix that is the same.
|
| FindPairMoleculeIndexBetaN2 |
BETA-NITROGEN MODEL
Class to identify the pair of molecules that are the same in terms of displacement vector and orientation
This is done to speed up the construction of the Hessian Matrix such that we do not have to recalculate
the block matrix that is the same.
|
| FindTransitionTemperature |
Class that determines the transition properties for alpha and beta nitrogen
|
| FiniteDifferenceDerivativeCGNitrogenBeta |
Finite Difference Derivative Class that is used by Conjugate Gradients related classes
This class returns the potential energy and the first derivative of lattice energy
PAY ATTENTION to variable: fixedDeltaU
|
| HarmonicAlphaNitrogenModel | |
| HarmonicAlphaNitrogenModelDecomposed |
Class that constructs the Hessian Matrix
Special features about this class is that:
1.
|
| HarmonicAlphaNitrogenModelLatticeSum |
Lattice sum class for Alpha-phase Nitrogen
|
| HarmonicAlphaNitrogenModelPairMolecule | |
| HarmonicAlphaNitrogenModelPairMoleculeSequential |
This class is created to take care of Java out of memory problem when creating
a 2D array that is gigantic [~10000][~10000]
The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules
This class also applied the molecules pair identification algorithm to speed up the
matrix construction.
|
| HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2 |
This class is created to take care of Java out of memory problem when creating
a 2D array that is gigantic [~10000][~10000]
The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules
This class also applied the molecules pair identification algorithm to speed up the
matrix construction.
|
| HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS |
This class is created to take care of Java out of memory problem when creating
a 2D array that is gigantic [~10000][~10000]
The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules
This class also applied the molecules pair identification algorithm to speed up the
matrix construction.
|
| HarmonicAlphaNitrogenModelPairMoleculeSequentialLS |
This class is created to take care of Java out of memory problem when creating
a 2D array that is gigantic [~10000][~10000]
The class is write a 5 x (nA * dof) Matrix to file while looping through the molecules
This class also applied the molecules pair identification algorithm to speed up the
matrix construction.
|
| HarmonicBetaNitrogenModel |
Beta-phase Nitrogen Harmonic Approximation
with only 3 translational degrees of freedom
|
| HarmonicBetaNitrogenModelDecomposed |
Class that constructs the Hessian Matrix
Special features about this class is that:
1.
|
| HarmonicBetaNitrogenModelLatticeSum |
Lattice sum class for Beta-phase Nitrogen
|
| HarmonicBetaNitrogenModelPairMoleculeSequential |
Beta-phase Nitrogen Harmonic Approximation
with only 3 translational degrees of freedom
|
| HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS |
Beta-phase Nitrogen Harmonic Approximation
with only 5 degrees of freedom
with lattice sum
|
| HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2 |
Beta-phase Nitrogen Harmonic Approximation
with only 3 translational degrees of freedom
|
| HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS |
Beta-phase Nitrogen Harmonic Approximation
with only 3 translational degrees of freedom
with lattice sum
|
| HarmonicBetaNitrogenModelPairMoleculeSequentialLS |
Beta-phase Nitrogen Harmonic Approximation
with only 3 translational degrees of freedom
with lattice sum
|
| HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS |
Disordered alpha-phase
This class is created to take care of Java out of memory problem when creating
a 2D array that is gigantic [~10000][~10000]
The class is write a 3 x (nA * dof) Matrix to file while looping through the molecules
This class also applied the molecules pair identification algorithm to speed up the
matrix construction.
|
| HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS |
Disordered alpha-phase
This class is created to take care of Java out of memory problem when creating
a 2D array that is gigantic [~10000][~10000]
The class is write a 3 x (nA * dof) Matrix to file while looping through the molecules
This class also applied the molecules pair identification algorithm to speed up the
matrix construction.
|
| LatticeSumCrystalMolecular |
Lattice sum crystal for molecular model
|
| MCMoveMoleculeCoupledInitPert |
Standard Monte Carlo molecule-displacement trial move.
|
| MCMoveMoleculeCoupledSuperBox |
Standard Monte Carlo molecule-displacement trial move for superbox.
|
| MCMoveRotateMolecule3DConstraint |
MCMoveRotate that moves the molecules according to pre-set constraint angle
which is given by the parameter "angle"
This class does not consider rotational energy, so the variable "energyChange"
always returns zero
getB() always returns positive one is to ensure the proposed move is always
accepted
|
| MCMoveRotateMolecule3DFixedAngle |
MCMoveRotate that moves the molecules according to pre-set constraint angle
which is given by the parameter "angle"
This class does not consider rotational energy, so the variable "energyChange"
always returns zero
getB() always returns positive one is to ensure the proposed move is always
accepted
the proposed angle criteria is based on u3 and u4 distribution
|
| MCMoveRotateMolecule3DN2AveCosThetaConstraint |
Impose constraint to prevent the alpha-N2 phase from becoming orientationally-disordered
the constraint imposed is the average cosine theta, where
theta is the orientation angle off the molecular nominal orientation
|
| MCMoveRotateMolecule3DSuperBox |
MC Rotate Move 3D for superbox
The potential master that being passed in this class is a "full-strength" potential without
multiplying by 0.5 for the speciesA and speciesB interaction.
|
| MCMoveVolumeN2 |
Monte Carlo volume-change move for simulations in the NPT ensemble.
|
| MeterBoltzmann |
Meter used for overlap sampling in the target-sampled system.
|
| MeterBoltzmannDirect |
Meter used for overlap sampling in the target-sampled system.
|
| MeterBoltzmannRotPerturb |
Meter used for overlap sampling in the target-sampled system.
|
| MeterDirectInitPert |
Meter used for overlap sampling in the target-sampled system.
|
| MeterNormalizedCoord |
Sample the distribution of the normalized coordinate for the atoms/ molecules
from coordinate definition, calcU method.
|
| MeterNormalizedCoordBeta |
Sample the distribution of the normalized coordinate for the atoms/ molecules
from coordinate definition, calcU method.
|
| MeterOrientationDistribution |
Meter that measures the spherical coordinate angles
angle[0]: is theta, angle between the projection vector (molecular axis vector onto xy plane)
and x-axis
angle[1]: is phi, angle between the molecular axis vector and z-axis
|
| MeterOrientationOrderParameter |
Meter used to sample orientation order parameter
|
| MeterRotationDistributionGroup |
Meter that measures the spherical coordinate angles
angle[0]: is theta, angle between the projection vector (molecular axis vector onto xy plane)
and x-axis
angle[1]: is phi, angle between the molecular axis vector and z-axis
|
| MeterRotPerturbMolecule |
Meter that returns a Boltzmann factor difference between 2 systems: system 1 and 0
1: (Target System) sampled with an angle constraint, e.g.
|
| MeterTargetRPMolecule |
Rotational Perturbation for beta-phase Nitrogen
- scaling of the rotational angle to better map the phase space
of the perturbing systems.
|
| MeterTargetTPMolecule |
For molecular model, e.g., diatomic Nitrogen model, with 5 d.o.f.
|
| MinimizationBetaNitrogenModel |
Lattice-Energy Minimization for Beta-Nitrogen Structure
using gradient
|
| MinimizationBetaNitrogenModelLS |
Lattice-Energy Minimization for Beta-Nitrogen Structure
using gradient with lattice sum
|
| MinimizeBetaNitrogenLatticeParameter |
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
|
| MinimizeBetaNitrogenLatticeParameterFromFile |
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
|
| MinimizeBetaNitrogenLatticeParameterLSFromFile |
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
|
| MinimizeBetaNitrogenTranslationDOF |
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are all the translational d.o.f of the molecules
NO rotational d.o.f.
|
| MinimizeGammaNitrogenLatticeParameter |
Determine c/a ratio for tetragonal unit cell that minimizes
the lattice energy of gamma-N2 crystal structure
|
| P0LatticeEnergyCorrec |
The lattice energy correction for Nitrogen model
zero-body interaction
All the parameters are determined from the fitted equation.
|
| P2Nitrogen |
P2 6-point potential for Nitrogen.
|
| P2NitrogenAB |
P2 6-point potential for Nitrogen.
|
| P2NitrogenAnisotropic |
P2 6-point potential for Nitrogen with anisotropic contribution
Reference: 1.
|
| P2NitrogenShellModel |
CAUTION!!!!!! The potential DOES NOT really describe the ALPHA and GAMMA structure at
NON-ZERO temperature condition!!
(through observation [SimulationGraphic]
and pressure calculation[MeterPressureMolecular])
P2 shell-model potential for Nitrogen.
|
| PRotConstraint | |
| SimDirectBetaN2RP |
Direct Sampling for Rotational Perturbation
|
| SimDirectBetaN2RP.SimOverlapParam |
Inner class for parameters understood by the SimOverlapBetaN2RP constructor
|
| SimDirectBetaN2RPAngleToNoAngle |
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
|
| SimDirectBetaN2RPInitPert |
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
|
| SimDirectDisorderedAlphaN2RPInitPert |
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
|
| SimOverlapAlphaN2TP |
Temperature-perturbation simulation for alpha-phase Nitrogen
|
| SimOverlapAlphaN2TP.SimOverlapParam |
Inner class for parameters understood by the HSMD3D constructor
|
| SimOverlapBetaN2RP | |
| SimOverlapBetaN2RP.SimOverlapParam |
Inner class for parameters understood by the SimOverlapBetaN2RP constructor
|
| SimOverlapBetaN2RPScaling |
rotational-perturbation simulation for beta-phase Nitrogen with angle scaling
however, one can set parameter "doScaling" to FALSE if scaling not desirable
|
| SimOverlapBetaN2RPScaling.SimOverlapParam |
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
|
| SimOverlapBetaN2TP |
Temperature-perturbation simulation for beta-phase Nitrogen
|
| SimOverlapBetaN2TP.SimOverlapParam |
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
|
| SimOverlapDisorderedAlphaN2RPScaling |
rotational-perturbation simulation for beta-phase Nitrogen with angle scaling
however, one can set parameter "doScaling" to FALSE if scaling not desirable
|
| SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam |
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
|
| SimOverlapDisorderedAlphaN2TP |
Temperature-perturbation simulation for disordered alpha-phase Nitrogen
|
| SimOverlapDisorderedAlphaN2TP.SimOverlapParam |
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
|
| SimOverlapNitrogenModel |
Simulation to run sampling with the nitrogen model to find the free energy difference
between the harmonic reference system and the target system
The Bennett's Overlapping Sampling Simulation
- used to check for the computation time
|
| SimOverlapNitrogenModel.SimOverlapParam |
Inner class for parameters understood by the HSMD3D constructor
|
| SimulationAlphaNitrogenModel |
Simulation class for nitrogen molecules
alpha-N2 crystal Structure
|
| SimulationBetaNitrogenModel |
Simulation class for nitrogen molecules
beta-N2 crystal Structure
|
| SimulationBetaNitrogenModelTest |
Simulation class for nitrogen molecules
beta-N2 crystal Structure
|
| SimulationGammaNitrogenModel |
Simulation class for nitrogen molecules
gamma-N2 crystal Structure
|
| SpeciesN2 |
Species nitrogen molecule
with 4-points charges
|
| SpeciesN2ShellModel |
Species nitrogen molecule (shell model)
Reference: Fabianski R.
|
| TestRotationVector |